First you need to generate a force field for that molecule using quantum calculations. Then you need to prepare three file 1) .pdb file, 2) .itp file and 3) .top file.
ATB and PRODRG servers have this facilities, you can go to their website and submit your molecule in a pdb format (use gaussview/avogadro for this).
Hi,
Lot of thanks for your reply.
While running this, it takes very very long time. How can we reduce time?
Should we change dt and nsteps simultaneously?
This is the production file, in order to calculate RDF.
integrator = md
dt = 0.002 ; 2 fs
nsteps = 5000000 ; 10.0 ns
nstenergy = 5000
nstlog = 5000
nstxout-compressed = 2000
continuation = yes
constraint-algorithm = lincs
constraints = h-bonds
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = Cut-off
rvdw = 1.0
DispCorr = EnerPres
tcoupl = Nose-Hoover
tc-grps = System
tau-t = 2.0
ref-t = 298.15
nhchainlength = 1
pcoupl = Parrinello-Rahman
tau_p = 2.0
compressibility = 4.46e-5
ref_p = 1.0
10 ns in production phase MD is reasonably long. You can reduce nsteps. Be sure of your objectives while choosing rest of the paraeters in mdp file. Good luck.
Dear John,
If you want to simulate an unknown molecule (i.e, unknown to the package you are using, that can be Gromacs, NAMD etc.) you have to provide the force field and topology of that molecule. If it is incorporated in the package then you won't need one. Otherwise you have to include the topology and the force field manually, that is the nonbonded interaction parameters for LJ potential. Here quantum chemistry calculations are needed.
Hope my answer will suffice !
Thank you.
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